[gmx-users] Check for bad contacts and/or reduce the timestep

Dear all I have simulated my system 7 different temperature from 300K~500K.Every time I simulated for 10ns. But when I run the simulation above 500K (I.e 530K/550K/560K) the simulation was crash in NPT equilibrium stage with following warning. *step XXX: Water molecule starting at atom can no

[gmx-users] how to creat ligand topology to minimize in vacuo in the absence of the protein

Dear gmx-usersI need to create a topology for my designed drug as a ligand to minimize it in the vacuo in the absence of the protein. But I dont know how can i convert the DRG.itp file which I obtained from PRODRG site to a .top file . I searched in the Google and found " Re: minimizing ligand o

Re: [gmx-users] Check for bad contacts and/or reduce the timestep

Hi, Parrinello Rahman is not a great choice for the first stages of equilbration, as suggested at e.g. http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation. Your choice of temperature coupling groups is also an anti-pattern, e.g. http://www.gromacs.org/Documentation/Terminolo

Re: [gmx-users] Can't locate state.cpt for gmx mdrun

Hello Justin, I see now why there aren't checkpoint files being produced. I guess I wanted to checkpoint files, in case the EM didn't converge in n steps, then I could keep going from that point instead of starting over with >n steps. Thanks for the response. Yonatan On Fri, Jul 7, 2017 at 8:14

[gmx-users] Regarding getting the trajectories at certain time intervals

Hello, I have ran an md simulation which has 6 frames (3000 / 500 ie., nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps), and now i need to get the trajectories, but this will be of very huge data (which gives trajectories of interval of every 0.5 ps)...So how can i get the trajecto

[gmx-users] Fwd: Regarding getting the trajectories at certain time intervals

Hello, I have ran an md simulation which has 6 frames (3000 / 500 ie., nsteps / nstxout, nsteps = 0.001 * 3000 = 3 ps), and now i need to get the trajectories, but this will be of very huge data (which gives trajectories of interval of every 0.5 ps)...So how can i get the trajecto

Re: [gmx-users] Fwd: Regarding getting the trajectories at certain time intervals

Hi, Look at "gmx help trjconv" ;-) The b and e options aren't measured in frames, and another option is available for selecting frames at different time intervals. Mark On Mon, 10 Jul 2017 06:06 Dilip H N wrote: > Hello, > I have ran an md simulation which has 6 frames (3000 / 500 ie.

Re: [gmx-users] protein protein interaction: side chain contribution

Hi Justin, Thanks a lot for the valuable advice. "A society with free knowledge is better than a society with free food" On Fri, Jul 7, 2017 at 3:04 PM, Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi Justin, > Thanks a lot for the advice. It looks like I had put one at

Re: [gmx-users] (no subject)

Hi, You can't do that with normal gromacs. But googling may reveal options. Mark On Sat, 8 Jul 2017 14:07 Shivangi Agarwal wrote: > hello to all > > How can i perform PBSA in gromacs > > > Thanks in advance > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.groma

Re: [gmx-users] Generating GROMACS input file from the GAMESS output file

Thank you Justin Every time your comment helped me. I should compare two system that are Zn_binding protein and Fe_binding protein. So I need force field that satisfies the following conditions. First, force field contains two metal ion (Fe and Zn)information. Second, force field contain metal io